Zinc (Zn) has been classified as a 'Specific Pollutant' under Annex VIII of the EU Water Framework Directive by two thirds of the EU member states. As a result, the UK Environmental Quality Standard (EQS) for Transitional and Coastal (TrAC) Waters has been reduced from 612 nM to 121 nM total dissolved Zn. It is widely accepted that the free metal ion ([Zn2+]) is the most bioavailable fraction, but there are few techniques available to determine its concentration in these waters. In this work, Absence of Gradients and Nernstian Equilibrium Stripping (AGNES) has been applied, for the first time, to determine [Zn2+] in estuarine waters. The AGNES method had a mean RSD of +/- 18%, a (deposition time dependent) limit of detection of 0.73 nM and a [Zn2+] recovery of 112 +/- 19% from a certified reference material (BCR-505; Estuarine Water). AGNES results for 13 estuarine samples (salinity 0.1-31.9) compared well (P = 0.02) with Competitive Ligand Exchange Cathodic Stripping Voltammetry (CLE-AdCSV) except for one sample. AGNES requires minimal sample manipulation, is unaffected by adsorption of interfering species at the electrode surface and allows direct determination of free zinc ion concentrations. Therefore AGNES results can be used in conjunction with ecotoxicological studies and speciation modelling to set and test compliance with water quality standards.